Only the staunchest Pirate fanboy can deny that Ninja have some level of awesome. Any story that can reasonably fit Ninja in there, like stories in Feudal Japan, or the fantasy equivalent, will do so. Sometimes, those fantasy equivalents seem to exist solely to give them a reason to include the Ninja.

Then again, some stories can't easily fit them, but throw them in anyway. It doesn't have to make sense. It's freakin' Ninja in your story! If you want to have them involved the battle of Gettysburg, go ahead. They just won't be recorded in the history books, because Ninja are masters of invisibility.

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Anime & Manga

While Hughes Gouli is usually just an ordinary mecha pilot in Overman King Gainer he occasionally awesome puts on his ninja suit and starts kicking ass

New Getter Robo features an arc where the main characters go to an alternate-universe version of Heian-era Japan, apparently just as an excuse to include ninja in a Humongous Mecha anime. One of these includes a 200ft tall ninja Oni, which doesn't sound very stealthy but is nonetheless quite awesome.

See also Volfogg for another ninja mech. But unlike the Getter Robo example, he's a main character.

As if the acrobatics in Claymore weren't already enough, two minor characters include two knights who jump around on rooftops and throw knives at people. One of them is a standard lightweight rogue... the other is wearing a full suit of armor.

A popular first-season fan theory for Code Geass was that Sayoko, Lelouch and Nunnally's maid, was secretly a ninja who was as talented a fighter as Suzaku. The staff said Sure Why Not, and in the second season she was revealed as a Badass ninja clan heiress who almost fought the cyborg Jeremiah Gottwald to a standstill.

Not just in the second season - in the audio commentary for one episode, Satomi Arai comments that throughout the first season the writers would tease her about "Sayoko's true power" but frustratingly never gave her the chance to shine.

Byakuya Kuchiki from Bleach has a group of bodyguard Ninjas, as seen in the Omakes.

Of course, Soifon manages to subvert this trope when she summons her squad of ninjas to deal with Yoruichi in the Soul Society arc. Guess she forgot about the Conservation of Ninjutsu.

One could say Ash is quite the ninja at times, in the movies at least. In the first movie he does that cool flip thing when he gets knocked down when he attacks Mewtwo by himself, how he flips off of wooden posts in the wall and catches the Jewel of Life in said movie (while being who knows how far above the ground?). They wanted the movies to be awesome, thus they made Ash a ninja.

Comic Books

Sin City: "Deadly little Miho. You won't feel a thing unless she wants you to. She twists the blade. He feels it."

One of the classic moments from Mark Waid's run on The Flash; our hero is out at a restaurant with his girlfriend, who is showing signs of wanting to talk about their relationship. Suddenly, ninjas attack!

Psylocke of the X-Men is practically the Anthropomorphic Personification of this trope. As the equally British sister of Captain Britain, she was moderately attractive and loved by fans... but when she was put into a female ninja's body, her attractiveness and popularity went through the roof, as she became the team's Ms. Fanservice.

Similarly, Kitty Pryde, during a trip to Japan, was abducted and Mind Screwed by the demonic Ogun, who downloaded a lifetime's worth of experience into her head, turning her Brainwashed and Crazy. Once she got her mind back, she retained much of her ninja skills.

One issue of the Astro City "Dark Ages" story arc starts off with a martial arts fight between two kung-fu superheroes and a team of flying jetpack ninjas.

Film

Ella Enchanted has the Crimson Guard, which is basically a group of MEDIEVAL NINJAS. In a European fantasy kingdom. Given the other anachronisms already shown (bat-ox, anybody?), it's not that farfetched. The fact that they are summoned by breaking the glass on a button box just makes it better.

Ninjas appear in Speed Racer. Oddly enough, they attack the Japanese racing team, rather than working with them as one might expect a ninja to do.

James Bond: Do you have any commandos here?Tiger Tanaka: I have much, much better. Ninjas.

The Last Samurai. The movie is going along like "Dances with Samurai" when suddenly a Ninja vs. Samurai battle breaks out halfway through the movie.

In Kevin Smith's review of The Passion of the Christ, he suggests that instead of the same old story, the movie starts with Jesus on the cross, and then ninjas (with uzis) come and and rescue him. When Jesus protests that he is supposed to die, one of the ninja yells, "Not on my watch!"

Vin Diesel film The Pacifier featured ninjas as home invaders in a relatively family-friendly film. They were actually North Korean terrorists.

The driving logic behind the Godfrey Ho Ninja Movies, which takes existing film and splices in ninja scenes woven into the plot via dubbing.

Literature

In the Fighting Fantasy book Deathtrap Dungeon, one of your competitors is a ninja despite the book being set in pseudo-medieval Europe.

To be fair the text just refers to him as a "black-robed assassin" -- it was the artist who drew him as a ninja.

On the other hand, when you finally fight him, the name before his stats specifically labels him as a ninja.

Erast Fandorin exiles himself to Japan after the disastrous ending of the first novel. Guess whom he meets there and learns crazy martial arts from...

The Yahtzee NaNoWriMo novel Fog Juice starts with the protagonist being chased by ninjas. The actual plot of the novel is the result of a desperate action he takes to get away from them—namely, drinking Fog Juice, which is guaranteed to solve any problems you have now (the ninjas) and replace them with interesting new ones.

Ninjas are hallmarks of works in the Cyberpunk genre, in spite of taking place in a high-tech future. In works written in the 80's, when Japan was about to take over the world, the Yakuza enforces its authority with vat-grown ninja assassins, often armed with high-tech versions of traditional weaponry.

Also spoofed in Witches Abroad. Magrat Garlick briefly takes up the martial arts, but being both a witch and a Lancre girl at heart she doesn't quite get what beating the stuffing out of people with your bare hands has to do with getting in touch with the universe and thinks "Ninja" would be a nice name for a girl.

Sisterhood series by Fern Michaels: Oh, yeah, the author has got that right! In the book The Jury, Jack Emery calls some in to beat down men with presidential gold shields. The book Final Justice has Bert's friends call them in to launch an attack on him and the soon to be stepping down FBI director, so that Bert will defend the director and get the position as FBI director!

Live Action TV

An episode of Angel featured ninja-cyborgs for no apparent reason, which blew up if you tried to examine their corpses uncautiously. It was awesome.

How I Met Your Mother: one of the character is talking about his work and a boring report. His friends complain about it... so he ends up calling it the "ninja report" instead, and everyone goes "Ninjas are awesome" everytime it's mentioned.

Spin City. Charlie daydreamed of winning the World Series, and fighting ninjas to make it more awesome.

Blue Heelers had a case where a mate of Tom's from Vietnam is found murdered, his wife is a Japanese national, and a witness claims to have seen someone clad head to toe in black. Nick amusingly but in all earnestness suggests he was dressed like a ninja, making Tom think he would be transferred if he reported it.

The Moonlighting episode "Atomic Shakespeare" was a wild Anachronism Stewvery loosely based on The Taming of the Shrew. It included Petruchio being attacked by, first, Renaissance swordsmen, and second, four ninja (they were referred to as "kung fu assassins"), before he even spoke his first line.

Mad TV once had a Take That sketch directed at Steven Seagal, with the actor starring in a remake of Kung Fu. When Seagal completely botches Kwai Chang Caine's Zen philosophies, he distracts the issue by shouting "NINJAS!" which causes several ninja to attack him, resulting in a frustrated David Carradine walking off the set.

And from seasons without a ninja theme, Rocky, Adam, and Aisha were ninjas. Wild Force tries on the trope for size with the ninja Duke Org, Onikage. During his all too short tenure as The Dragon,[1] we even had ninja outfits on Toxica and Jindrax and even the footsoldiers. However, they served a purpose - the outfits let them board the Animarium undetected.

This goes double for the Alien Rangers arc of MMPR Season 3, where the Kakuranger suits were used. The Alien Rangers fishy Rubber Forehead Aliens from a distant water planet called Aquitar, but their battle footage comes from Kakuranger, so it's full of Hand Seals and Flash Step and other ninja-ness that defies the MMAR theme. There were two moments that serendipitously matched the water theme, though (Cestro runs on water in one episode, and creates a waterfall in another. You'll notice it's just him, the blue Ranger, who does that... just like Tori from Ninja Storm. In sentai it's for the same reasons - ninja Rangers have Magic Martial Arts, and Elemental Powers often accompany those.)

Kamen Rider Fourze. Its theme is astronomy, and you've got a Rider with a rocket-shaped helmet and a base on the moon fighting constellation-themed villains. What are the Mooks? Ninjas. Why? Because they can.

In "Tangled Web" of RL Stine's The Nightmare Room" anything the protagonist claims comes true. He says he has ninja bodyguards.

Music

During the early days of DragonForce, ZP Theart and Sam Totman established a side band, Shadow Warriors, as a gag project and a general parody of indie bands then prevalent on mp3.com. The band was presented as a quartet of heavy metal ninjas.

There's also the bonus track from Ultra Beatdown, the truely awesome Strike of the Ninja.

The music video for The Presidents of the United States' song "Peaches" features the band playing in a peach grove until the mid-way point, when they are suddenly attacked by ninjas. They spend the rest of the video locked in martial arts combat.

Then again, this is in a world in which two common character archetypes are "Street Samurai" and "Physical Adept" (almost always described as "magic ninja" in the flavor text, and possibly possessing some ninja-like abilities). However the fact that every named game had "ninja" squeezed into the title appeared to be invoking this trope.

The Dungeons & Dragons 3.5 rulebook Complete Adventurer introduced the Ninja base class, just for this trope (unfortunately the class just kind of falls flat compared to a good rogue or monk).

Video Games

Way back in Final Fantasy I, when your characters got their classes upgraded, the Thief suddenly became a Ninja.

Any Final Fantasy that uses a ninja job class (or Samurai and Monk for that matter). Occasionally handwaved as a job from a foreign land, but there still seem to be an extraordinary number of ninja running around medieval-Europe-inspired Ivalice in Final Fantasy Tactics, and, as mentioned above, often there's no token Far East village to justify it, mentioned or otherwise.

Mass Effect 3's Cerberus Phantoms provide a straighter example. They're basically cybernetic ninjas, cartwheeling around the battlefield until they get close enough to shank you. This follows with the increased focus on Melee combat in the third game.

There's also Kai Leng, the Illusive Man's new enforcer, another cyborg who favors Sword and Gun style.

As mentioned above, the Fuschia Gym in the first and second generations of Pokemon games. In the third gen, there's a trainer class called the Ninja Boy; and the fifth gen has the Bug type Accelgor and the Shadow Triad.

Secret Agent has both Ninjas and Ninja Masters, two kinds of Mooks. The Ninja, clad in black, is the fastest mook in the game and deals typical Collision Damage with its nunchucks. The Ninja Master wears blue and is slower, but has a gun instead of nunchucks. Apparently, the true master of ninjutsu is one who realized that there's no point in using traditional melee weapons when ordinary firearms are more effective.

The Golden Sun series has a set of Ninja classes among its Class and Level System options, available in full to Venus and Mars Adepts while the Ninja class itself is also available to Jupiter Adepts. It's usually one of the best combat options for Squishy Wizard types, since it gives them a high Attack multiplier, useful boosts to Defense, Agility, and Hit Points, and its only detriments are to Luck and Psy Points, which these characters typically already have in abundance, but it's quite tricky to access and maintain, since it requires a lot of Djinin and unleashing even one of them can result in a class change to something less favorable.

According to Buck Godot: Zap Gun for Hire ninjas are just about the only thign every sentient species has in common. Many aliens species have wildly different definitions for such basic concepts as rest, food or death, yet every single one of them has a type of warrior that fits the "ninja archetype". Usually they tend to dress in black pajamas and wield katanas.

Schlock Mercenary: In the Mallcop Command plotline, a ninja unexpectedly shows up and starts jumping his way through the shopping mall.

NJ from Electric Wonderland uses the screenname "Night Ninja". When Trawn asked him what "NJ" stood for, he answered, "NinJa, I think..." (A later comic revealed that the "N" actually stands for "Nate".)

Although we haven't seen ninjas in Grrl Power, the trope is referenced.

Richard Han of Survival of the Fittest, while not actually a ninja, goofs off and pretends to be one for most of his time on the island. Which makes his first appearance on the island (being stuck in a tree) and his death by misstepping and falling off a mountain that much more funnier.

G1 Transformers had the episode Enter the Nightbird, a Transformers-sized female ninja robot, made by a Japanese scientist to benefit society. Yeah, watch those nunchucks 'benefitting' their way through society all through the episode.

Used twice in U.S. Acres: first, the instance on the quote page, where Orson adds ninjas to Rumplestiltskin to please Booker and Sheldon. In another episode, those two decide to retell The Tortoise and Hare. They consider turning the tortoise into a ninja, but reconsider, saying "Who would want to seethat?"

A third instance came up before those two: When Orson reads them a gender-swapped version of "Cinderella", they insists that the stepsisters stepbrothers be ninjas.

Bubbles, the Big Bad in the Chip 'n Dale Rescue Rangers episode "The Case of the Cola Cult", has Ninja mice as Mooks. Although Gadget disposes of them quickly, they do add to the amount of awesome in the episode.

The Fairly OddParents: Timmy fights ninjas after he wishes the world was like an action movie. Also: Ninja Bunnies!

In Avatar: The Last Airbender, Katara and Zuko dress in all black and stealth their way around several Fire Nation navy commands, seen by no one until they attack, in order to get information on the man that killed Katara's mother. It's all kinds of bad-ass.

The Dai Li are Earthbending Ninjas. While they don't do the all black attire normally attributed to the profession, the training and combat style they use fits the bill perfectly. Given that unlike most Earthbenders, or any capable bender in the series, they use hidden weapons and misdirection in their combat style.

Also, Zuko in Blue Spirit mode. Silent, stealthy, wears all black, incredibly badass, one of the only characters to be actually deadly in each appearance... total ninja right there.

"If you don't want to end up like him *the training dummy he just demolished*, then do as I say."

MAD sketches occasionally contain this trope and they do it with a humourous style.

There was recently a quick sketch named 'Everything is Better With Ninjas'. Indeed.

The original G.I. Joe had Storm Shadow (Snake Eyes hadn't been outed as one in time for the original cartoon) who was by far one of the most popular characters of the time. The new series follows in the comic's footsteps, making Snake Eyes a full-blown ninja in addition to Storm Shadow, and has the young female ninja Jinx for good measure.

The Problem Solverz episode "Hide and Seek Ninjaz". In it, the solverz must rescue a girl's mother who was captured by ninjas. They then face off against the rainbow-clad head ninja in a life-or-death match of hide-and-seek.